I would finish the last classes and introduce level 5 and 6 class upgrades.

This alone will generate large encounter re-balance checklists.

Intrigue: I would probably begin mapping out plenty of Easter egg side-quests and inspirations. There is way too much information on the Wiki to spoil the fun.

I loved the floor puzzle I had to solve to enter the under-dark, it was very characteristic of pen and paper game mechanics.

Perhaps (for replay value and a unique experience)...a system that completely shuffles the clues for these quests:

Books being placed on random shelves

Runes that can only be reveled by detect magic or other means, such as a special device.
The runes could be randomly placed and randomly picked (say 5 clues from a larger set that doesn't repeat on the next play-through).
So not predictable either.

NPCs that are randomly picked to participate in the hunt (next time it will be other NPCs).

portals that require special keys (like in planescape, where
any arch could be a portal, and that spoon might be the key).

Use of spells...."The way in is obviously this blocked passage"...hmm perhaps gaseous form.

DM inspiration points will be awarded.